autoplot(prcomp(t(mcp_zscore_matrix)), data = person_metadata_df, colour = 'person', main = "MCPCounter")

autoplot(prcomp(t(mcp_zscore_matrix)), data = person_metadata_df, colour = 'cell_type', main = "MCPCounter")

autoplot(prcomp(t(cs_zscore_matrix)), data = person_metadata_df, colour = 'person', main = "Cibersort")

autoplot(prcomp(t(cs_zscore_matrix)), data = person_metadata_df, colour = 'cell_type', main = "Cibersort")

pheatmap(
mcp_zscore_matrix,
main = "MCPCounter",
annotation_row = mcp_heatmap_row_df,
annotation_col = mcp_heatmap_col_df,
scale = "none")

pheatmap(
cs_zscore_matrix,
main = "Cibersort",
annotation_col = mcp_heatmap_col_df,
scale = "none")

kable(mcp_result_df)
| T cells |
13.8292755 |
0.9653426 |
18.0546530 |
0.0079474 |
21.1208562 |
2.1961531 |
34.3130702 |
31.0723570 |
64.3336642 |
110.8644786 |
221.5502480 |
| CD8 T cells |
0.1044257 |
0.0000000 |
0.1144199 |
0.0000000 |
5.1480786 |
3.5415684 |
9.9586084 |
0.0000000 |
25.4858351 |
0.0000000 |
0.0000000 |
| Cytotoxic lymphocytes |
2.8650014 |
0.2164809 |
0.4099724 |
0.0000000 |
5.0368322 |
0.0000000 |
127.9298351 |
0.1132905 |
3.8932443 |
53.7292123 |
5.8935111 |
| NK cells |
0.6357623 |
1.1450994 |
2.0403135 |
0.0000000 |
0.5577085 |
0.0406549 |
17.3850143 |
0.2555213 |
0.0222527 |
0.9405487 |
0.0782516 |
| B lineage |
2481.5315250 |
0.3873194 |
128.5530097 |
0.0886628 |
30.5502987 |
15.7810464 |
2.9325842 |
94.1196600 |
18.1666949 |
0.4736888 |
0.3039038 |
| Monocytic lineage |
8.4573807 |
4.4268619 |
32.7316174 |
0.0265289 |
23.9040232 |
0.5908418 |
15.1087143 |
10.7185267 |
1.8697219 |
4.1096415 |
20.9601860 |
| Myeloid dendritic cells |
0.5765238 |
2.4619812 |
0.0323942 |
0.2421462 |
106.4240804 |
0.0000000 |
0.0323203 |
0.8329225 |
1.6702145 |
24.7167584 |
0.0000000 |
| Neutrophils |
20.5790657 |
22.3305318 |
18.7862939 |
8.6250564 |
6.6263891 |
13.0897145 |
27.8710753 |
12.9548885 |
24.5172605 |
2.8520772 |
182.4263920 |
| Endothelial cells |
2.9168239 |
15.3186873 |
0.9363362 |
1.5290548 |
1.7832275 |
7.0728664 |
4.3108516 |
1.8967228 |
5.7432010 |
5.1042425 |
4.4457599 |
| Fibroblasts |
1.5148395 |
103.9436579 |
0.3104304 |
70.6748973 |
26.8494087 |
0.0459198 |
303.8642751 |
1.0218086 |
0.4600203 |
95.1860144 |
435.0542083 |
kable(cs_result_df)
| B.cells.naive |
0.0324249 |
0.0109948 |
0.0000000 |
0.0000000 |
0.0752762 |
0.0000000 |
0.0155335 |
0.0000000 |
0.0205709 |
0.0000000 |
0.0199688 |
| B.cells.memory |
0.0000000 |
0.0000000 |
0.0063887 |
0.0000000 |
0.0000000 |
0.0598007 |
0.0000000 |
0.0370316 |
0.0000000 |
0.0000000 |
0.0000000 |
| Plasma.cells |
0.0473771 |
0.0000000 |
0.0008949 |
0.0000000 |
0.0293307 |
0.0044725 |
0.0090820 |
0.0155085 |
0.0000000 |
0.0101017 |
0.0062959 |
| T.cells.CD8 |
0.5361031 |
0.0006400 |
0.0183396 |
0.0000000 |
0.1673104 |
0.0000000 |
0.1920935 |
0.0106082 |
0.1732509 |
0.0414166 |
0.0000000 |
| T.cells.CD4.naive |
0.0000000 |
0.1286951 |
0.0000000 |
0.0370675 |
0.0000000 |
0.2217144 |
0.0000000 |
0.0116718 |
0.0000000 |
0.0000000 |
0.0000000 |
| T.cells.CD4.memory.resting |
0.0000000 |
0.0445111 |
0.0179172 |
0.3154697 |
0.1766933 |
0.2540471 |
0.0000000 |
0.4148627 |
0.4841043 |
0.1484929 |
0.2049672 |
| T.cells.CD4.memory.activated |
0.0893417 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0795550 |
0.0000000 |
0.0658341 |
0.3356031 |
0.1180163 |
0.0148216 |
0.2507235 |
| T.cells.follicular.helper |
0.0470317 |
0.0000000 |
0.0175408 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0299156 |
0.0000000 |
0.0568229 |
0.0355081 |
0.0665547 |
| T.cells.regulatory..Tregs. |
0.0000000 |
0.0000000 |
0.0000000 |
0.0813446 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
| T.cells.gamma.delta |
0.0022534 |
0.0000000 |
0.0610650 |
0.0793380 |
0.0000000 |
0.2062707 |
0.0239566 |
0.0000000 |
0.0279861 |
0.0000000 |
0.0056172 |
| NK.cells.resting |
0.0000000 |
0.0719079 |
0.0000000 |
0.0000000 |
0.0187349 |
0.0000000 |
0.0000000 |
0.0323334 |
0.0642258 |
0.0000000 |
0.0000000 |
| NK.cells.activated |
0.0373345 |
0.0000000 |
0.0481145 |
0.0398817 |
0.0000000 |
0.0000000 |
0.3295948 |
0.0000000 |
0.0000000 |
0.4159811 |
0.1229230 |
| Monocytes |
0.0128247 |
0.4244302 |
0.0000000 |
0.0000000 |
0.0103271 |
0.0000000 |
0.0034563 |
0.0163080 |
0.0043653 |
0.0136778 |
0.0100214 |
| Macrophages.M0 |
0.0000000 |
0.1487772 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
| Macrophages.M1 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0448319 |
0.0000000 |
0.0059163 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0069890 |
| Macrophages.M2 |
0.0226498 |
0.0388808 |
0.0893910 |
0.0000000 |
0.0924293 |
0.0039942 |
0.0151936 |
0.0083860 |
0.0001223 |
0.0090362 |
0.0245820 |
| Dendritic.cells.resting |
0.0040118 |
0.0000000 |
0.0000000 |
0.0000000 |
0.1143003 |
0.0000000 |
0.0000000 |
0.0061772 |
0.0000000 |
0.0090394 |
0.0107591 |
| Dendritic.cells.activated |
0.0000000 |
0.0000000 |
0.0350956 |
0.0583733 |
0.0729468 |
0.0358320 |
0.0060190 |
0.0007664 |
0.0072328 |
0.0313241 |
0.0071882 |
| Mast.cells.resting |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0591832 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
| Mast.cells.activated |
0.1520148 |
0.0542089 |
0.6713359 |
0.2283382 |
0.0068086 |
0.1826323 |
0.2897604 |
0.1107432 |
0.0256478 |
0.2517119 |
0.2442204 |
| Eosinophils |
0.0166326 |
0.0769540 |
0.0250936 |
0.1153551 |
0.0961636 |
0.0253198 |
0.0122401 |
0.0000000 |
0.0176545 |
0.0176363 |
0.0168808 |
| Neutrophils |
0.0000000 |
0.0000000 |
0.0088232 |
0.0000000 |
0.0009409 |
0.0000000 |
0.0073205 |
0.0000000 |
0.0000000 |
0.0012523 |
0.0023088 |
| P.value |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
9999.0000000 |
| Correlation |
0.1222714 |
0.0290433 |
0.1093780 |
0.0117757 |
0.2109025 |
-0.0004476 |
0.5804317 |
0.1731422 |
0.2737427 |
0.3564176 |
0.4973030 |
| RMSE |
1.0865307 |
1.0929230 |
1.2344680 |
1.1165663 |
0.9915465 |
1.1306945 |
0.8319734 |
1.0365532 |
1.0157390 |
1.0237864 |
0.8683398 |